It is the oldest and largest music school in the country, tracing its origins back to 1829 when the Zagreb Musical Society's school (German: Tonschule des Agramer Musikvereines) was established, at a time when Croatia was part of the Austrian Empire.

After World War II the Academy was officially recognized as an institution of higher education and in 1979 it became part of the University of Zagreb.

[1] At the time the school comprised primary, secondary and tertiary levels of musical education.

The Academy had signed a 100-year lease contract with the City of Zagreb in 2009, which also agreed to provide half of the HRK 210 million (€27.5 million) funding spent to restore the building (with the other half provided by the University of Zagreb and the Croatian Ministry of Science, Education and Sports).

[3] The restored building occupies some 12.000 square meters spread over three underground and eight ground levels, and hosts 7 departments of the Academy with its 150 full-time employees, several dozen contractors and 550 students.